Take the argument to the extreme and consider something like and iphone 5s. It has a tiny sensor so everything is always in focus. But it still has an f2 lens in terms of light transition. So sometimes I can get a better macro shot in low light on my 5s than I could on my 5d mk iii. Because to get an equivalent depth of field I'd have to stop down to f18 which would push up the ISO to extreme.
I think you have to factor in the difference in sensor size and light gathering capabilities of both. I don't know the exact factor but I would say that the FF sensor would gather a lot more light than the iPhone sensor at the exact same exposure settings. Well that part is obvious but then you see, when you stop the FF / lens aperture down a few stops to match the amount of light you have essentially "bought" yourself a few stops of ISO too. Then another feature of the FF is that even at ultra high ISO it will be relatively noise free and have more detail.
I've never tried macro with an iPhone using only ambient light. I'd imagine you'd need a lot of light. It would be interesting to see a side by side comparison with a 5D3.